Clementine has some powerful tools, many of which I don't quite understand
Clementine always had a right click Delete option, which now reads Delete From Disk, I blew up a few files accidentally learning the clementine definition of delete
I've never used the right click organize files choice
I guess that it organizes whatever files on the playlist you have highlighted
The Organize Files when copying to device, allows you to reorder the file names of the files on the external media or player to suit the specific requirements
Clementine expects your music library to be organized Artist[folder]>Album[folder]>Song[file]
I generally just create a folder [album] & give it a name for random files
Best of collections with various artists, I just put the songs with their artist or make the artist whoever the collection is a tribute to
Another method is to give the collection a custom Genre, Group or Comment tag
I use duplicate, alternate version & live as genre to filter for playlist building
The devs are not on this forum
You can find them on Github